Yes, having recently gone through most of the protein modification data
currently in the archive, the PDB biocurators have overall been very
consistent with the handling of protein modifications. Despite this,
inconsistencies have accumulated over the years. In the current project,
we are adding new annotation and detailed documentation to support the
future biocuration of new protein modifications. We hope that this will
ensure consistency is maintained in the future.
Best,
Marcus
On 24/06/2024 17:32, Frances C. Bernstein wrote:
For those who do not know, I worked on data processing for the PDB
from 1974 to 1998 (entries 15 to ~9000) and we tried to be consistent
in representing small modifications to amino acids: modified amino
acid vs. standard amino acid plus het group. With the then lack of
software tools we struggled to remember whether we had encountered a
similar case before. And there is the additional issue to consider of
how the depositor views the modification and discusses it in their
publications. I am glad to know that the PDB will be standardizing
the data representation of these cases.
Frances
On 2024-06-24 12:11, Marcus Bage wrote:
Hi Frances,
This is one of the central issues being addressed as part of the
protein modifications project.
When the PDB archive is updated as part of the project rollout, all
protein modifications will be grouped into distinct categories of
modification. The category they fall in determines how they will be
handled throughout the archive.
In general, small, well-described protein modifications will be
handled as part of the modified amino acid group. For example
phosphorylations, methylations and acetylations.
Modifications that that are large, branched or that link multiple
protein residues will be handled as linked het groups. For example
carbohydrates, hemes, lipids and crosslinkers.
This approach will make it easier to ensure that all modification
groups are handled in a single consistent way throughout the archive.
A significant effort is being made to standardise protein
modifications in all existing entries to ensure that this will be the
case for the whole archive.
For more detailed information about this project please see:
github.com/wwPDB/protein-modification-extension
Kind Regards,
Marcus
On 24/06/2024 16:44, f...@marbuta.pair.com wrote:
Would it be possible for the PDB to explain the distinction in
representation between the case of a modified amino acid and the
case of additional atoms bound to the side chain of a standard amino
acid. If it is a standard amino acid will the extra atom(s) always
be represented as a het group? Is the PDB consistent through all
entries in such a case?
Frances Bernstein
On 2024-06-24 11:03, Marcus Bage wrote:
Hi everyone,
Last year wwPDB standardised the backbone atom names for all
residues that are part of a polypeptide sequence within the PDB
archive. A full list of all chemical components affected can be
found at:
github.com/wwPDB/backbone-extension/tree/master/data/ccds
This is a list of all modified amino-acid residues and non-standard
peptide residues within the PDB archive. It was last updated in
August 2023.
wwPDB is in the process of standardising and enriching all protein
modification data in the PDB archive. As part of this, all modified
peptide residues will have data added to their CCD definition file
to describe in what way the residue is modified. For example, the
3-letter code SEP, will have the information to state that it is
the phosphorylation of serine. Once this information is released it
will be considerably easier to access such information in the archive.
A detailed description of the changes being made as part of the PTM
standardisation project can be found at:
github.com/wwPDB/protein-modification-extension
Kind regards,
Marcus
On 24/06/2024 15:21, Harry Powell wrote:
Hi folks
“Can of worms” is how this could be described!
From various different sources (many thanks Paul, Mitch, Robbie)
I have now managed to obtain (inter alia) lists of 31, 189, 863
and 916 modified amino acids - and there are other, longer (and
possibly shorter and equimetric [is that even a word?] lists that
I could create if I want to be more comprehensive! It’s certainly
_possible_ that some of the members of an individual list are
duplicates, but for my current purposes these should suffice
nearly all the time (and for those cases where the list falls
short, I would expect people to raise the issue directly with me…)
Once more, I knew this would be the place to ask!
Harry
On 24 Jun 2024, at 13:40, Robbie Joosten
<robbie_joos...@hotmail.com> wrote:
Hi Harry,
A BSc student in our lab just had a look at this. Here is the
list of mappings pdb-redo uses:
https://github.com/PDB-REDO/pdb-redo-main/blob/trunk/tools/pdb-redo-data.cif
(second to last loop).
Cheers,
Robbie
pdb-redo-main/tools/pdb-redo-data.cif at trunk ·
PDB-REDO/pdb-redo-main
core pdb-redo script, tools and data files. Contribute to
PDB-REDO/pdb-redo-main development by creating an account on GitHub.
github.com
From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of
Harry Powell <0000193323b1e616-dmarc-requ...@jiscmail.ac.uk>
Sent: Monday, June 24, 2024 2:03 PM
To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK>
Subject: [ccp4bb] List of 3-letter codes of modified amino acids
Hi
An internet search doesn’t yield an obvious list of these (I did
find a paper DOI:10.1016/j.jmgm.2006.08.004 that says there are
293, but the link included appears to be dead -
http://deposit.pdb.org/hetdictionary.txt).
I’m almost convinced that this has been asked here previously (if
not recently), but a quick search through ccp4bb postings has not
revealed it to me.
Can anyone help?
Harry
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